Rename k to q

I have renamed almost all instances of k to q, even rho_j_k. Also the output now contains q instead of k, which required some changes to the test that compares the old and new command line output.

The file /examples/Diatomic_Chain/analyze_output.py still contains k because the output file that is used there contains k too, but the examples should be reviewed anyway. I don't think it's even possible to run the example bash-scripts at the moment, so maybe the final instances of k there could be sorted out in another issue when the examples are reviewed?

Closes #53 (closed)